--- imach/src/imach.c	2002/02/20 17:08:52	1.15
+++ imach/src/imach.c	2002/02/20 17:15:02	1.17
@@ -85,7 +85,7 @@ double jmean; /* Mean space between 2 wa
 double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;
-FILE *ficgp, *fichtm,*ficresprob;
+FILE *ficgp, *fichtm,*ficresprob,*ficpop;
 FILE *ficreseij;
   char filerese[FILENAMELENGTH];
  FILE  *ficresvij;
@@ -1150,10 +1150,10 @@ void lubksb(double **a, int n, int *indx
 } 
 
 /************ Frequencies ********************/
-void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)
+void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint)
 {  /* Some frequencies */
  
-  int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+  int i, m, jk, k1, k2,i1, j1, bool, z1,z2,j;
   double ***freq; /* Frequencies */
   double *pp;
   double pos;
@@ -1161,7 +1161,7 @@ void  freqsummary(char fileres[], int ag
   char fileresp[FILENAMELENGTH];
 
   pp=vector(1,nlstate);
- probs= ma3x(1,130 ,1,8, 1,8);
+  probs= ma3x(1,130 ,1,8, 1,8);
   strcpy(fileresp,"p");
   strcat(fileresp,fileres);
   if((ficresp=fopen(fileresp,"w"))==NULL) {
@@ -1192,13 +1192,16 @@ void  freqsummary(char fileres[], int ag
 	       bool=0;
 	 }
 	  if (bool==1) {
-	   for(m=fprev1; m<=lprev1; m++){
+	    for(m=fprev1; m<=lprev1; m++){
+	     k2=anint[m][i]+(mint[m][i]/12.);
+	     if ((k2>=1984) && (k2<=1988.5)) {
 	     if(agev[m][i]==0) agev[m][i]=agemax+1;
 	     if(agev[m][i]==1) agev[m][i]=agemax+2;
 	     freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 	     freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
-	   }
-	 }
+	     }
+	    }
+	  }
        }
         if  (cptcovn>0) {
 	 fprintf(ficresp, "\n#********** Variable "); 
@@ -1860,6 +1863,7 @@ int main()
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
   char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
+  char popfile[FILENAMELENGTH];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
   int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */
@@ -1867,8 +1871,9 @@ int main()
   int ju,jl, mi;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
-  int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast;
+  int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;
   int hstepm, nhstepm;
+  int *popage;
 
   double bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;
@@ -1882,7 +1887,8 @@ int main()
   double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;
-  double kk1;
+  double kk1, kk2;
+  double *popeffectif,*popcount;
 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];
@@ -1898,7 +1904,7 @@ int main()
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
 
 
-  printf("\nIMACH, Version 0.64b");
+  printf("\nIMACH, Version 0.7");
   printf("\nEnter the parameter file name: ");
 
 #ifdef windows
@@ -1955,6 +1961,8 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   ungetc(c,ficpar);
   
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);
+  fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);
+ 
  while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
@@ -1964,6 +1972,18 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   ungetc(c,ficpar);
   
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);
+  fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);
+     
+  
+while((c=getc(ficpar))=='#' && c!= EOF){
+    ungetc(c,ficpar);
+    fgets(line, MAXLINE, ficpar);
+    puts(line);
+    fputs(line,ficparo);
+  }
+  ungetc(c,ficpar);
+  
+  fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);
  
   covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0; 
@@ -2273,8 +2293,8 @@ printf("Total number of individuals= %d,
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
-    free_matrix(mint,1,maxwav,1,n);
-    free_matrix(anint,1,maxwav,1,n);
+    /* free_matrix(mint,1,maxwav,1,n);
+       free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
 
@@ -2306,21 +2326,15 @@ printf("Total number of individuals= %d,
        }
      }
    } 
-
-
-   /*for(i=1; i <=m ;i++){ 
-     for(k=1; k <=cptcovn; k++){
-       printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
-     }
-     printf("\n");
-   }
-   scanf("%d",i);*/
     
    /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
-  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);
-
-    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint);
+  
+  free_matrix(mint,1,maxwav,1,n);
+  free_matrix(anint,1,maxwav,1,n);
+  
+  pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
@@ -2335,8 +2349,10 @@ printf("Total number of individuals= %d,
     }
     
     /*--------- results files --------------*/
-    fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);
-    
+    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);
+   fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased); 
+   fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);
+
    jk=1;
    fprintf(ficres,"# Parameters\n");
    printf("# Parameters\n");
@@ -2618,7 +2634,7 @@ chdir(path);
     printf("Problem with %s \n",optionfilehtm);goto end;
   }
 
- fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\"> 
+ fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\"> 
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
 Total number of observations=%d <br>
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
@@ -2813,8 +2829,25 @@ fclose(fichtm);
   agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */ 
+  
+  if (popforecast==1) {
+    if((ficpop=fopen(popfile,"r"))==NULL)    {
+      printf("Problem with population file : %s\n",popfile);goto end;
+    } 
+    popage=ivector(0,AGESUP);
+    popeffectif=vector(0,AGESUP);
+    popcount=vector(0,AGESUP);
+
+    i=1;   
+    while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
+      {
+	i=i+1;
+      }
+    imx=i;
+  
+  for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+  }
 
-   k=0;
   for(cptcov=1;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;
@@ -2825,22 +2858,26 @@ fclose(fichtm);
       fprintf(ficresf,"******\n");
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+      if (popforecast==1)  fprintf(ficresf," [Population]");
 
       for (agedeb=fage; agedeb>=bage; agedeb--){ 
-	fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);
+	fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);
        if (mobilav==1) {
 	for(j=1; j<=nlstate;j++) 
-	  fprintf(ficresf," %.5f ",mobaverage[(int)agedeb][j][cptcod]);
+	  fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);
 	}
 	else {
 	  for(j=1; j<=nlstate;j++) 
-	  fprintf(ficresf," %.5f ",probs[(int)agedeb][j][cptcod]);
+	  fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);
 	}  
-      for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");
+
+       for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");
+       if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);
       }
-      for (cpt=1; cpt<=nforecast;cpt++)   
+      
+      for (cpt=1; cpt<=nforecast;cpt++) { 
+	fprintf(ficresf,"\n");
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-	
 	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 	nhstepm = nhstepm/hstepm; 
 	/*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
@@ -2852,24 +2889,35 @@ fclose(fichtm);
 	for (h=0; h<=nhstepm; h++){
 	
 	 if (h*hstepm/YEARM*stepm==cpt)
-	    fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);
+	    fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);
 	 
 	  
-	  for(j=1; j<=nlstate+ndeath;j++) {
-	    kk1=0.;
-	    for(i=1; i<=nlstate;i++) {	      
-	      if (mobilav==1)
-	      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];
-	      else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];
-	    }    
-	  if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);
+	 for(j=1; j<=nlstate+ndeath;j++) {
+	   kk1=0.;kk2=0;
+	   for(i=1; i<=nlstate;i++) {	      
+	     if (mobilav==1) 
+		kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];
+	     else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];
+	     if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
+	    }
+	   if (h*hstepm/YEARM*stepm==cpt) {
+	     fprintf(ficresf," %.3f", kk1);
+	       if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
+	   }
 	  }
 	}
 	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	
+      }
       }
     }
   }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  if (popforecast==1) {
+    free_ivector(popage,0,AGESUP);
+    free_vector(popeffectif,0,AGESUP);
+    free_vector(popcount,0,AGESUP);
+  }
   free_imatrix(s,1,maxwav+1,1,n);
   free_vector(weight,1,n);
   fclose(ficresf);